Job ID = 16439580 SRX = SRX9518333 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8262210 spots for SRR13070816/SRR13070816.sra Written 8262210 spots for SRR13070816/SRR13070816.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439670 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:41 8262210 reads; of these: 8262210 (100.00%) were paired; of these: 4320044 (52.29%) aligned concordantly 0 times 1686848 (20.42%) aligned concordantly exactly 1 time 2255318 (27.30%) aligned concordantly >1 times ---- 4320044 pairs aligned concordantly 0 times; of these: 96340 (2.23%) aligned discordantly 1 time ---- 4223704 pairs aligned 0 times concordantly or discordantly; of these: 8447408 mates make up the pairs; of these: 8174640 (96.77%) aligned 0 times 66169 (0.78%) aligned exactly 1 time 206599 (2.45%) aligned >1 times 50.53% overall alignment rate Time searching: 00:13:41 Overall time: 00:13:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1249849 / 4030049 = 0.3101 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:51:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 15:51:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:51:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:51:42: 1000000 INFO @ Tue, 02 Aug 2022 15:51:50: 2000000 INFO @ Tue, 02 Aug 2022 15:51:59: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:52:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 15:52:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:52:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:52:06: 4000000 INFO @ Tue, 02 Aug 2022 15:52:12: 1000000 INFO @ Tue, 02 Aug 2022 15:52:14: 5000000 INFO @ Tue, 02 Aug 2022 15:52:21: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:52:21: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:52:21: #1 total tags in treatment: 2713027 INFO @ Tue, 02 Aug 2022 15:52:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:52:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:52:21: #1 tags after filtering in treatment: 1729029 INFO @ Tue, 02 Aug 2022 15:52:21: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 15:52:21: #1 finished! INFO @ Tue, 02 Aug 2022 15:52:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:52:21: #2 number of paired peaks: 493 WARNING @ Tue, 02 Aug 2022 15:52:21: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Tue, 02 Aug 2022 15:52:21: start model_add_line... INFO @ Tue, 02 Aug 2022 15:52:21: start X-correlation... INFO @ Tue, 02 Aug 2022 15:52:22: end of X-cor INFO @ Tue, 02 Aug 2022 15:52:22: #2 finished! INFO @ Tue, 02 Aug 2022 15:52:22: #2 predicted fragment length is 139 bps INFO @ Tue, 02 Aug 2022 15:52:22: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 02 Aug 2022 15:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.05_model.r WARNING @ Tue, 02 Aug 2022 15:52:22: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:52:22: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 02 Aug 2022 15:52:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:52:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:52:24: 2000000 INFO @ Tue, 02 Aug 2022 15:52:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.05_summits.bed INFO @ Tue, 02 Aug 2022 15:52:27: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:52:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 15:52:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:52:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:52:35: 3000000 INFO @ Tue, 02 Aug 2022 15:52:40: 1000000 INFO @ Tue, 02 Aug 2022 15:52:46: 4000000 INFO @ Tue, 02 Aug 2022 15:52:48: 2000000 INFO @ Tue, 02 Aug 2022 15:52:56: 3000000 INFO @ Tue, 02 Aug 2022 15:52:56: 5000000 INFO @ Tue, 02 Aug 2022 15:53:03: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:53:06: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:53:06: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:53:06: #1 total tags in treatment: 2713027 INFO @ Tue, 02 Aug 2022 15:53:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:53:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:53:06: #1 tags after filtering in treatment: 1729029 INFO @ Tue, 02 Aug 2022 15:53:06: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 15:53:06: #1 finished! INFO @ Tue, 02 Aug 2022 15:53:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:53:06: #2 number of paired peaks: 493 WARNING @ Tue, 02 Aug 2022 15:53:06: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Tue, 02 Aug 2022 15:53:06: start model_add_line... INFO @ Tue, 02 Aug 2022 15:53:06: start X-correlation... INFO @ Tue, 02 Aug 2022 15:53:06: end of X-cor INFO @ Tue, 02 Aug 2022 15:53:06: #2 finished! INFO @ Tue, 02 Aug 2022 15:53:06: #2 predicted fragment length is 139 bps INFO @ Tue, 02 Aug 2022 15:53:06: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 02 Aug 2022 15:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.10_model.r WARNING @ Tue, 02 Aug 2022 15:53:06: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:53:06: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 02 Aug 2022 15:53:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:53:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:53:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:53:10: 5000000 INFO @ Tue, 02 Aug 2022 15:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.10_summits.bed INFO @ Tue, 02 Aug 2022 15:53:12: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 345 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:53:17: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:53:17: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:53:17: #1 total tags in treatment: 2713027 INFO @ Tue, 02 Aug 2022 15:53:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:53:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:53:17: #1 tags after filtering in treatment: 1729029 INFO @ Tue, 02 Aug 2022 15:53:17: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 15:53:17: #1 finished! INFO @ Tue, 02 Aug 2022 15:53:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:53:17: #2 number of paired peaks: 493 WARNING @ Tue, 02 Aug 2022 15:53:17: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Tue, 02 Aug 2022 15:53:17: start model_add_line... INFO @ Tue, 02 Aug 2022 15:53:17: start X-correlation... INFO @ Tue, 02 Aug 2022 15:53:17: end of X-cor INFO @ Tue, 02 Aug 2022 15:53:17: #2 finished! INFO @ Tue, 02 Aug 2022 15:53:17: #2 predicted fragment length is 139 bps INFO @ Tue, 02 Aug 2022 15:53:17: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 02 Aug 2022 15:53:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.20_model.r WARNING @ Tue, 02 Aug 2022 15:53:17: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:53:17: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 02 Aug 2022 15:53:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:53:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:53:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:53:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:53:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:53:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:53:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518333/SRX9518333.20_summits.bed INFO @ Tue, 02 Aug 2022 15:53:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 336 millis CompletedMACS2peakCalling